PXD000331

PXD000331 is an original dataset announced via ProteomeXchange.

Title	Critical assessment of proteome-wide label-free absolute abundance estimation strategies
Description	There is a great interest in reliable ways to obtain absolute protein abundances at a proteome-wide scale. To this end, label-free LC-MS/MS quantification methods have been proposed where all identified proteins are assigned an estimated abundance. Several variants of this quantification approach have been presented, based on either the number of spectral counts per protein or MS1 peak intensities. Equipped with several datasets representing real biological environments, containing a high number of accurately quantified reference proteins, we evaluate five popular low cost and easily implemented quantification methods (APEX, emPAI, iBAQ, Top3 and MeanInt). Our results demonstrate considerably improved abundance estimates upon implementing accurately quantified reference proteins; i.e. using spiked in SIS peptides or a standard protein mix, to generate a properly calibrated quantification model. We show that only the Top3 method is directly proportional to protein abundance over the full quantification range and is the preferred method in the absence of reference protein measurements. Additionally, we demonstrate that spectral count based quantification methods are associated with higher errors than MS1 peak intensity based methods. Furthermore, we investigate the impact of mis-cleaved, modified and shared peptides as well as protein size and the number of employed reference proteins on quantification accuracy. The .raw data submitted to PRIDE correspond to replicate DDA LC-MS/MS analysis of the UPS2 mix (Universal Proteomics Standard, UPS2, Sigma-Aldrich), as well as triplicate DDA LC-MS/MS analysis of the UPS2 mix spiked into samples from the following organisms M. pneumoniae, L. interrogans and D. melanogaster. The accompanying R-script called calculatePQIs.R was used to calculate the different Quantification Indices, provided that the peptide XICs or Spectral Counts have been loaded into a data.frame R object (which can be produced by SafeQuant).
HostingRepository	PRIDE
AnnounceDate	2014-08-08
AnnouncementXML	Submission_2014-08-08_00:31:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Mycoplasma pneumoniae; NCBI TaxID: 2104; scientific name: Leptospira interrogans; NCBI TaxID: 173; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-09 05:49:59	ID requested
1	2013-11-15 03:56:31	announced
1	2013-11-15 03:59:00	announced
2	2014-07-25 01:21:37	announced	Updated project metadata.
⏵ 3	2014-08-08 00:31:07	announced	Updated project metadata.

Ahrn, é E, Molzahn L, Glatter T, Schmidt A, Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics, 13(17):2567-78(2013) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: UPS2

Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/11/PXD000331

PRIDE project URI

• PRIDE
  1. PXD000331
     1. Label: PRIDE project
     2. Name: Critical assessment of proteome-wide label-free absolute abundance estimation strategies